Study of protonated dimers of cytosine, cytidine, and deoxycytidine using survival yield method and quantum mechanics calculations

RationaleCytosine and its conjugates are prone to form protonated, triply-bonded dimers. Therefore, the nucleic-acid cytosine-rich sequence forms the four-stranded noncanonical secondary structure known as the intercalated motif (i-motif). This process has resulted in studies on cytosine protonated dimers. This communication focuses on the protonated dimers of cytosine and its nucleoside using the survival yield (SY) method and quantum mechanics calculations.MethodsTo obtain the precursor ion fragmentation curve, the plot of SY against Ecom delta, the product ion spectra of the protonated dimers were obtained using a Waters/Micromass Q-TOF Premier mass spectrometer. Quantum mechanics calculations were performed using GAUSSIAN 16, and full geometry optimizations and energy calculations were performed within the density functional theory framework at B3LYP/6-31G(d,p).ResultsThe precursor ion fragmentation curve allowed the rating of the gas-phase stabilities of the analyzed protonated dimers. Substitution of sugar moiety at N1 cytosine atom decreased the gas-phase stabilities of the protonated dimers. The deoxycytidine dimer was found to be more stable than the cytidine dimer and cytidine-deoxycytidine dimer. Quantum chemical calculations indicated that cytosine aminohydroxy tautomer may be involved in the formation of protonated cytosine-cytosine nucleoside dimers but not in the formation of cytosine dimers.ConclusionsThe results obtained for nucleoside dimers indicated that the SY method may reflect the i-motif stabilities observed under physiological conditions. Therefore, the analysis of other protonated dimers of variously substituted cytosine-cytosine nucleoside using the SY method may be important to study the effect of cytosine substitution on the i-motif stabilities. Cytosine tautomer containing C2-OH horizontal ellipsis N(2H)-C4 moiety may be involved in the formation of protonated cytosine-cytosine nucleoside dimers.

Automated summary

This study focused on the protonated dimers of cytosine and its nucleoside, using experimental and quantum mechanics methods to investigate their gas-phase stabilities. The results showed that substitution of sugar moiety at N1 cytosine atom decreased the stability of the protonated dimers, and the deoxycytidine dimer was more stable than the cytidine dimer. Quantum chemical calculations suggested that a cytosine aminohydroxy tautomer may play a role in the formation of protonated cytosine-cytosine nucleoside dimers.